Magnesium in PDB 1i7j: Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding.

The structure of Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding., PDB code: 1i7j was solved by D.A.Adamiak, W.R.Rypniewski, J.Milecki, R.W.Adamiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.19
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	24.805, 24.805, 77.372, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / n/a

The binding sites of Magnesium atom in the Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding. (pdb code 1i7j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding., PDB code: 1i7j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:20.9 occ:0.56 O A:HOH225 1.7 27.3 0.7 O A:HOH229 1.7 38.1 0.7 O A:HOH228 1.9 14.3 0.2 O A:HOH224 1.9 23.5 0.4 OP1 A:OMG2 2.1 26.4 1.0 O A:HOH226 2.2 26.2 0.6 P A:OMG2 3.4 20.0 1.0 O3' A:OMC1 3.9 19.5 1.0 O A:HOH230 4.1 17.9 0.5 OP2 A:OMG2 4.1 21.0 1.0 H5'' A:OMG2 4.3 24.2 1.0 O5' A:OMG2 4.6 18.6 1.0 C5' A:OMG2 4.8 20.2 1.0 H5' A:OMG2 4.9 24.2 1.0 H5'' A:OMC1 5.0 32.2 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:12.2 occ:0.39 OP1 A:OMC5 1.9 17.8 1.0 O A:HOH219 2.1 31.6 0.7 O A:HOH221 2.4 24.8 0.6 P A:OMC5 3.4 15.7 1.0 H5'' A:OMC5 3.9 18.0 1.0 O A:HOH215 4.0 36.7 0.7 O3' A:OMG4 4.0 14.5 1.0 OP2 A:OMC5 4.2 17.9 1.0 O5' A:OMC5 4.4 14.3 1.0 C5' A:OMC5 4.5 15.0 1.0 H5' A:OMC5 4.5 18.0 1.0 O A:HOH207 4.6 25.9 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:55.6 occ:0.53 O A:HOH212 1.9 26.2 1.0 O A:HOH222 1.9 29.4 0.6 O A:HOH208 2.1 19.7 0.6 O A:HOH218 2.4 27.7 0.8 HN42 A:OMC5 3.7 16.6 1.0 O A:HOH217 4.0 23.4 1.0 H5 A:OMC5 4.1 14.0 1.0 O A:HOH209 4.1 19.1 0.8 N4 A:OMC5 4.3 13.8 1.0 O6 A:OMG6 4.4 14.9 1.0 O A:HOH202 4.5 19.5 1.0 N7 A:OMG6 4.6 13.2 1.0 C5 A:OMC5 4.6 11.7 1.0 HN41 A:OMC5 4.8 16.6 1.0 C4 A:OMC5 4.8 13.2 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:23.1 occ:0.45 O B:HOH221 2.0 27.6 0.7 O B:HOH227 2.0 30.0 0.8 OP1 B:OMG2 2.0 25.2 1.0 O B:HOH232 2.1 32.7 0.8 O B:HOH222 2.2 44.4 0.4 O B:HOH219 2.2 26.8 0.6 P B:OMG2 3.3 20.2 1.0 O3' B:OMC1 3.8 20.4 1.0 O B:HOH220 3.9 34.4 0.8 OP2 B:OMG2 4.0 21.4 1.0 H5'' B:OMG2 4.4 23.1 1.0 O5' B:OMG2 4.5 19.4 1.0 H5'' B:OMC1 4.5 28.3 1.0 C5' B:OMG2 4.8 19.3 1.0 H5' B:OMG2 4.9 23.1 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 2'-O-Me(Cgcgcg)2: An Rna Duplex at 1.19 A Resolution. 2-Methyl-2,4-Pentanediol and Magnesium Binding. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:23.3 occ:0.38 O B:HOH226 1.8 25.1 0.7 O B:HOH231 2.0 33.5 0.3 O B:HOH207 2.0 27.1 0.8 O B:HOH206 2.1 23.3 0.8 HN42 B:OMC5 3.6 16.3 1.0 O B:HOH208 3.9 19.3 0.7 H5 B:OMC5 4.0 15.7 1.0 O B:HOH234 4.1 22.4 0.6 N4 B:OMC5 4.2 13.6 1.0 O A:HOH227 4.2 30.8 0.7 O B:HOH204 4.4 18.8 1.0 O6 B:OMG6 4.4 14.7 1.0 C5 B:OMC5 4.6 13.1 1.0 N7 B:OMG6 4.6 12.4 1.0 HN41 B:OMC5 4.7 16.3 1.0 C4 B:OMC5 4.7 12.7 1.0 O B:HOH225 4.8 32.5 0.4

D.A.Adamiak, W.R.Rypniewski, J.Milecki, R.W.Adamiak. The 1.19 A X-Ray Structure of 2'-O-Me(Cgcgcg)(2) Duplex Shows Dehydrated Rna with 2-Methyl-2,4-Pentanediol in the Minor Groove. Nucleic Acids Res. V. 29 4144 2001.
ISSN: ISSN 0305-1048
PubMed: 11600703
DOI: 10.1093/NAR/29.20.4144